Alignments for a candidate for mmsB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Cupriavidus basilensis 4G11

Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate RR42_RS25640 RR42_RS25640 3-hydroxyisobutyrate dehydrogenase

Query= metacyc::MONOMER-11664
         (295 letters)



>FitnessBrowser__Cup4G11:RR42_RS25640
          Length = 298

 Score =  406 bits (1043), Expect = e-118
 Identities = 204/295 (69%), Positives = 238/295 (80%)

Query: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60
           M IAFIGLGNMGAPMA NL+KAGH L +FDL+   +A     G   + SP++AAA ++LV
Sbjct: 1   MEIAFIGLGNMGAPMAANLLKAGHALTVFDLDANAVAAALLAGATSAGSPREAAARADLV 60

Query: 61  ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120
           ITMLPAAAHVR VYL +DGVLAG RPG P VDCSTIDP T R V++AAA++     DAPV
Sbjct: 61  ITMLPAAAHVRQVYLGEDGVLAGARPGVPMVDCSTIDPATVRTVAEAAASQDSPFADAPV 120

Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGGTGGA AGTLTFMVGA   LF  ++PVL  MGRN+V CG  GTGQ+AKICNNLLLGIS
Sbjct: 121 SGGTGGAQAGTLTFMVGADQPLFERIRPVLLAMGRNVVPCGAPGTGQVAKICNNLLLGIS 180

Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240
           M+GVSEAMALG ALGID  VLAGIIN+STGRCWSSD+YNP+PG+   APA+RGY GGF A
Sbjct: 181 MMGVSEAMALGAALGIDPAVLAGIINTSTGRCWSSDSYNPYPGVQPAAPAARGYVGGFAA 240

Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYRKKD 295
           +LMLKDLGLAT+AARQAHQP+ +GA+AQQLYQ+MS +G G  DFSA ++ Y K+D
Sbjct: 241 DLMLKDLGLATDAARQAHQPLWMGALAQQLYQSMSQQGMGRLDFSACLKLYEKQD 295


Lambda     K      H
   0.317    0.134    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 362
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 295
Length of database: 298
Length adjustment: 26
Effective length of query: 269
Effective length of database: 272
Effective search space:    73168
Effective search space used:    73168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS25640 RR42_RS25640 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01692.hmm
# target sequence database:        /tmp/gapView.1745.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01692  [M=288]
Accession:   TIGR01692
Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-131  423.3   7.1   2.7e-131  423.2   7.1    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS25640  RR42_RS25640 3-hydroxyisobutyrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS25640  RR42_RS25640 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.2   7.1  2.7e-131  2.7e-131       1     287 [.       5     291 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 423.2 bits;  conditional E-value: 2.7e-131
                                 TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 
                                               fiGlGnmG+pmaanllkagha++vfdl+a+av  +  aGa+ a s+ ea++ ad vitmlPa++hv++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS25640   5 FIGLGNMGAPMAANLLKAGHALTVFDLDANAVAAALLAGATSAGSPREAAARADLVITMLPAAAHVRQV 73 
                                               9******************************************************************** PP

                                 TIGR01692  70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138
                                               y+g++g+la ++ +++++d+stid+ + r+vae+aa++   f+daPvsGG+gga+aGtltfmvG+ +  
  lcl|FitnessBrowser__Cup4G11:RR42_RS25640  74 YLGEDGVLAGARPGVPMVDCSTIDPATVRTVAEAAASQDSPFADAPVSGGTGGAQAGTLTFMVGADQPL 142
                                               ********************************************************************* PP

                                 TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207
                                               f+r +pvl amg+n+v +G+ G+Gq+akiCnnlllgism+Gv+ea+alg +lG+dp+vla i+++s+Gr
  lcl|FitnessBrowser__Cup4G11:RR42_RS25640 143 FERIRPVLLAMGRNVVPCGAPGTGQVAKICNNLLLGISMMGVSEAMALGAALGIDPAVLAGIINTSTGR 211
                                               ********************************************************************* PP

                                 TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276
                                               cWs+d+ynP+PGv ++aPa +gy gGfa++lmlkdlgla +aa+++++++ +Gala++ly+ ++++g+g
  lcl|FitnessBrowser__Cup4G11:RR42_RS25640 212 CWSSDSYNPYPGVQPAAPAARGYVGGFAADLMLKDLGLATDAARQAHQPLWMGALAQQLYQSMSQQGMG 280
                                               ********************************************************************* PP

                                 TIGR01692 277 kkdfsavikll 287
                                               ++dfsa +kl+
  lcl|FitnessBrowser__Cup4G11:RR42_RS25640 281 RLDFSACLKLY 291
                                               ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (298 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.80
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources